Merge pull request 'Add Pubmed affiliations (inferred by BIP) as actionsets' (#353) from 9117_pubmed_affiliations into beta

Reviewed-on: #353
This commit is contained in:
Claudio Atzori 2023-11-22 13:53:07 +01:00
commit 836d7ec724
5 changed files with 58 additions and 25 deletions

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@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String crossrefInputPath = parser.get("crossrefInputPath");
log.info("crossrefInputPath: {}", crossrefInputPath);
final String pubmedInputPath = parser.get("pubmedInputPath");
log.info("pubmedInputPath: {}", pubmedInputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
isSparkSessionManaged,
spark -> {
Constants.removeOutputDir(spark, outputPath);
prepareAffiliationRelations(spark, inputPath, outputPath);
List<KeyValue> collectedFromCrossref = OafMapperUtils
.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
spark, crossrefInputPath, collectedFromCrossref);
List<KeyValue> collectedFromPubmed = OafMapperUtils
.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
spark, pubmedInputPath, collectedFromPubmed);
crossrefRelations
.union(pubmedRelations)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
});
}
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
String outputPath) {
private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
String inputPath,
List<KeyValue> collectedfrom) {
// load and parse affiliation relations from HDFS
Dataset<Row> df = spark
@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations
df
return df
.toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> {
@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
qualifier,
Double.toString(row.getAs("confidence")));
List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
// return bi-directional relations
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
.map(p -> new AtomicAction(Relation.class, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
}
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

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@ -6,9 +6,15 @@
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramName": "cip",
"paramLongName": "crossrefInputPath",
"paramDescription": "the path to get the input data from Crossref",
"paramRequired": true
},
{
"paramName": "pip",
"paramLongName": "pubmedInputPath",
"paramDescription": "the path to get the input data from Pubmed",
"paramRequired": true
},
{

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@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
# The following is needed as a property of a workflow
oozie.wf.application.path=${oozieTopWfApplicationPath}
inputPath=/data/bip-affiliations/data.json
crossrefInputPath=/data/bip-affiliations/data.json
pubmedInputPath=/data/bip-affiliations/pubmed-data.json
outputPath=/tmp/crossref-affiliations-output-v5

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@ -2,8 +2,12 @@
<parameters>
<property>
<name>inputPath</name>
<description>the path where to find the inferred affiliation relations</description>
<name>crossrefInputPath</name>
<description>the path where to find the inferred affiliation relations from Crossref</description>
</property>
<property>
<name>pubmedInputPath</name>
<description>the path where to find the inferred affiliation relations from Pubmed</description>
</property>
<property>
<name>outputPath</name>
@ -83,7 +87,7 @@
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
<name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
@ -96,7 +100,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

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@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest {
@Test
void testMatch() throws Exception {
String affiliationRelationsPath = getClass()
String crossrefAffiliationRelationPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String pubmedAffiliationRelationsPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String outputPath = workingDir.toString() + "/actionSet";
PrepareAffiliationRelations
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputPath", affiliationRelationsPath,
"-crossrefInputPath", crossrefAffiliationRelationPath,
"-pubmedInputPath", pubmedAffiliationRelationsPath,
"-outputPath", outputPath
});
@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
// );
// }
// count the number of relations
assertEquals(20, tmp.count());
assertEquals(40, tmp.count());
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result");
@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest {
// verify that we have equal number of bi-directional relations
Assertions
.assertEquals(
10, execVerification
20, execVerification
.filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList()
@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
Assertions
.assertEquals(
10, execVerification
20, execVerification
.filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList()